Main
Rui Fu
RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus
My research interests are in RNA degradation and post-transcriptional gene expression, interrogated through biochemical experiments and bioinformatic/computational analyses of genomic and sequencing data.
Education
Ph.D. Biological Science
University of California San Diego
La Jolla, CA, USA
2015 - 2009
B.S. Biological Science
Xiamen University
Xiamen, Fujian, China
2009 - 2005
Research Experience
Bioinformatic tool development:
clustifyr, automated single cell RNA-seq cell identity assignment Bioconductor package (author)
squirrelBox, RNA-seq data visualization, exploration, and analysis web browser built with R Shiny and JavaScript (author)
someta, quantification and monitoring of missing cell-level metadata in scRNA-seq GEO deposition (author)
scraps, scalable pipeline for extraction of polyadenylation site and sequencing internal priming information from scRNA-seq data (author)
valr, framework for tidyverse-style genomic interval analysis in R (co-developer)
Developed computational biology course materials:
rnabioco.github.io/practical-data-analysis
rnabioco.github.io/cellar
Semi-Independent Postdoctoral Informatics Fellow
Jay Hesselberth’s Supervision
University of Colorado Anschutz
Current - 2017
- Development of bioinformatics software packages for single cell RNA sequencing
- RNA post-transcriptional dynamics modeling of steroidogenesis <<<<<<< HEAD
- RNA-seq analysis and transcriptome annotation improvements for hibernating ground squirrel brain and liver =======
- RNA-seq analysis and transcriptome annotation improvements for hibernating ground squirrel brain >>>>>>> ed2b44cf86718946e816938d7dab92b40f2517a7
- Collaboration on various single cell RNA sequencing projects
- Analysis of human genetic variation from gnomAD database for insights into nonsense-mediated mRNA decay
Postdoctoral Research Fellow
Judy Lieberman’s Lab
Harvard Medical School
2017 - 2016
- Identification of a mitochondrial trigger for apoptotic mRNA decay
- Purification of cytotoxic granules and cytolytic proteins from NK cells
- Mouse genetic manipulation by CRISPR-Cas9, and automated genotyping with custom R app
Graduate Research Assistant
Jens Lykke-Andersen’s Lab
University of California San Diego
2015 - 2009
- Investigation of co-factors involved in ZFP36-mediated mRNA decay and translational repression during macrophage innate immune response
- Characterization of the ZFP36 family proteins in cell cycle progression regulation of mouse embryonic fibroblasts
Undergraduate Research Assistant
Ruichuan Chen’s Lab
Xiamen University
2009 - 2007
- Exploration of cell cycle and apoptosis implications of the transcription elongation regulator HEXIM1
- Mechanistic characterization of p-TEFb activation by HIV-Tat
Posters and Talks
Interactive scRNA-seq cell-type classification via clustifyr identifies widespread omission of cell-level annotations in public data repositories. (Keystone eSymposia on Single Cell Biology - Poster, co-present with mentee)
N/A
2021
Towards a comprehensive view of dynamic RNA regulation in hibernating 13-lined ground squirrel. (EMBL Conference, From Functional Genomics to Systems Biology - Poster)
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2020
ClustifyR: automated single-cell RNA sequencing cluster classification. (Keystone Symposia on Single Cell Biology - Poster)
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2019
PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA and poly(A)-tailed ncRNA during apoptosis. (Boston Children’s Hospital PCMM Research Poster Session - Poster)
N/A
2017
PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA during apoptosis. (Boston Children’s Hospital PCMM Research Poster Session - Poster)
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2016
TTP-mediated mRNA repression involves recruitment of the 4EHP-GYF2 complex. (Cold Spring Harbor Laboratory mRNA Processing Meeting - Presentation)
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2015
TTP represses translation of target mRNAs through the 4EHP-GYF2 complex. (UCSD Mechanisms of Gene Expression Seminar - Presentation)
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2014
TTP family proteins regulate the stability of retinoblastoma protein mRNAs during serum-stimulated G0-S transition. (Cold Spring Harbor Laboratory mRNA Processing Meeting - Poster)
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2013
The regulation of TTP family mRNA-decay factors during G0-S cell cycle progression. (Keystone Symposia on Protein-RNA Interactions - Poster)
N/A
2012
Teaching Experience
Online Lecture Instructor (Graduate-Level Courses)
University of Colorado Anschutz
N/A
- Informatics and Statistics for Molecular Biology (2020) - teaching and grading on RStudio Cloud platform
- Foundations in Biomedical Sciences (2020) - online lecture, paper discussion, and homework/exam design on RNA biology
- Workshop for scRNA-seq Data Analysis (2020) - course development and online lectures
Lecture Instructor (Graduate-Level Courses)
University of Colorado Anschutz
N/A
- Rigor in Research (2020) - lecture on RNA sequencing
- Foundations in Biomedical Sciences (2018, 2019) - lectures, paper discussion, and homework/exam design on RNA biology
- Practical Data Analysis with R/RStudio (2018, 2019) - course development and lectures
- Workshop for scRNA-seq Data Analysis (2019) - course development and lectures
Teaching Assistant (Graduate-Level Courses)
University of Colorado Anschutz
N/A
- Practical Computational Biology for Biologists: R (2018, 2019)
- Practical Computational Biology for Biologists: Python (2018, 2019)
- Core Topics in Biomedical Sciences (2018)
Weekly RNA Bioscience Initiative Informatics Office Hour
University of Colorado Anschutz
N/A
- Guidance on RNA and computational research questions from students and researchers of CU Anschutz Medical Campus
Teaching Assistant (Undergraduate-Level Courses)
University of California San Diego
N/A
- Molecular Biology (2012)
- DNA Recombination Lab (2011, 2012)
Mentoring Experience
RNA Bioscience Initiative Internship Mentoring
University of Colorado Anschutz
N/A
Current - 2020
- Mentoring of undergraduate computer science student for 2020 summer internship and beyond
- Project: systemic exploration of published scRNA-seq cell type signatures in the NCBI Gene Expression Omnibus
- Mentee’s work was integrated into updates to R Bioconductor packages clustifyr and clustifyrdatahub, GitHub repo someta, first author communication/essay manuscript, and poster presentation.
Summer Research Mentoring
Harvard Medical School
N/A
2017
- Mentoring of high school student enrolled in the MIT Research Science Institute program
- Topics: tissue culture, RNA-related bench experiments, RNA-seq informatics analysis, and scientific writing
BS/MS Student Research Mentoring
University of California San Diego
N/A
2015 - 2013
- Mentoring of student research spanning undergraduate honor thesis and master thesis on biochemical investigations of RNA-binding protein functions
- Project: biochemical investigation of RNA-binding protein functions
- Mentee’s work was integrated into second author 2016 RNA publication. Mentee was awarded Best Poster Presentation Award at 2014 UCSD Biological Sciences Annual Student Research Showcase.
Service and Training
Society memberships
RNA Society, International Society for Computational Biology, Genetics Society of America
N/A
Current - 2015
RNA Bioscience Initiative Grant Review
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N/A
Current - 2019
GENETICS Early Career Reviewer (Cellular Genetics section)
4 manuscripts reviewed for GENETICS and G3, tinyurl.com/rev-rf
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Current - 2018
Organizer for CU Anschutz Immuno-Informatics Joint Journal Club
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N/A
2020
Mentor Collective mentorship training
=======Organizer for UCSD Ethics Center’s Silent Spring (50th Anniversary) Project
>>>>>>> ed2b44cf86718946e816938d7dab92b40f2517a7N/A
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2019
Data Incubator Data Science Fellowship
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2017
Grant writing training under Dr Lieberman
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2016
Harvard Medical School Scientists Teaching Science Course
N/A
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2016
Diversity, Equity, and Inclusion Service
RNA Society Volunteer - Writer for Scientist Spotlight
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N/A
2021
CU Anschutz Medical Campus Equity Certificate Program training
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2021
Admissions Committee for CU Graduate Experiences for Multicultural Students
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2019
Mentor for CU Anschutz and Denver Campus ISCORE (undergraduate mentorship program)
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N/A
2019
Recognition
Dr Huang Memorial Scholarship, UC San Diego
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2011 - 2009
First-Class Scholarship
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2008 - 2006
XMU University Merit Student
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2008 - 2006
Science Outreach
Volunteer for CU Anschutz Medical Campus Young Hands in Science Outreach Program
tinyurl.com/younghandssci
N/A
2021
Facilitator at Denver Museum of Nature and Science - Prehistoric Journey section
N/A
N/A
2020 - 2019
Visitor Education Volunteer at the New England Aquarium
N/A
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2017 - 2016
Information Ambassador at the San Diego Zoo
N/A
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2016 - 2015
Organizer for UCSD Ethics Center’s Silent Spring (50th Anniversary) Project
N/A
N/A
2012
Disclaimer
Made with pagedown.
Code at github.com/raysinensis/cv.
<<<<<<< HEADLast updated on 2021-04-13.
=======Last updated on 2021-03-16.
>>>>>>> ed2b44cf86718946e816938d7dab92b40f2517a7